Happened to me too on trip to LHR. Just happened to be checking on this flight and noticed it said "choose seats"; I thought I already had but when I pulled up the seat chart it gave me business seats to choose from. So I also thought my SWUs had gone through and chose the seats. The next day I was back in Premium Economy and had lost my good original seats in that section and had to choose again with poorer choices.

Moral of the story is that just because it appears you've got an upgrade and can choose new seats doesn't necessarily mean that's really the case. In fact it can work against you because you might also lose your original choice of seats.